Merge remote-tracking branch 'upstream/main' into jabrefonline

* upstream/main:
  [Bot] Update CSL styles (JabRef#7824)
  Pin version of citeproc-java (JabRef#7827)
  JournalAbbreviation search feature (JabRef#7804)
  Bump fontbox from 2.0.23 to 2.0.24 (JabRef#7815)
  Revert "Bump org.eclipse.jgit (JabRef#7820)" (JabRef#7823)
  Bump bcprov-jdk15on from 1.68 to 1.69 (JabRef#7816)
  Bump postgresql from 42.2.20 to 42.2.21 (JabRef#7817)
  Bump org.eclipse.jgit (JabRef#7820)
  Bump mockito-core from 3.11.0 to 3.11.1 (JabRef#7819)
  Bump pdfbox from 2.0.23 to 2.0.24 (JabRef#7818)
  Bump byte-buddy-parent from 1.11.1 to 1.11.2 (JabRef#7821)
  Bump xmpbox from 2.0.23 to 2.0.24 (JabRef#7822)

CHANGELOG.md

@@ -26,7 +26,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added a feature that allows the user to open all linked files of multiple selected entries by "Open file" option. [#6966](https://github.com/JabRef/jabref/issues/6966)
 - We added a keybinding preset for new entries. [#7705](https://github.com/JabRef/jabref/issues/7705)
 - We added a select all button for the library import function. [#7786](https://github.com/JabRef/jabref/issues/7786)
-- We added auto-key-generation progress to the background task list. [#7267](https://github.com/JabRef/jabref/issues/7267)
+- We added a search feature for journal abbreviations. [#7804](https://github.com/JabRef/jabref/pull/7804)
+- We added auto-key-generation progress to the background task list. [#7267](https://github.com/JabRef/jabref/issues/72)
 
 ### Changed
 

build.gradle

@@ -120,17 +120,17 @@ dependencies {
     // Include all jar-files in the 'lib' folder as dependencies
     implementation fileTree(dir: 'lib', includes: ['*.jar'])
 
-    implementation 'org.apache.pdfbox:pdfbox:2.0.23'
-    implementation 'org.apache.pdfbox:fontbox:2.0.23'
-    implementation 'org.apache.pdfbox:xmpbox:2.0.23'
+    implementation 'org.apache.pdfbox:pdfbox:2.0.24'
+    implementation 'org.apache.pdfbox:fontbox:2.0.24'
+    implementation 'org.apache.pdfbox:xmpbox:2.0.24'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.8'
     implementation 'com.h2database:h2-mvstore:1.4.200'
 
     implementation group: 'org.apache.tika', name: 'tika-core', version: '1.26'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    implementation 'org.bouncycastle:bcprov-jdk15on:1.68'
+    implementation 'org.bouncycastle:bcprov-jdk15on:1.69'
 
     implementation 'commons-cli:commons-cli:1.4'
 
@@ -157,7 +157,7 @@ dependencies {
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.3'
 
-    implementation 'org.postgresql:postgresql:42.2.20'
+    implementation 'org.postgresql:postgresql:42.2.21'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -194,9 +194,7 @@ dependencies {
     implementation group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     annotationProcessor group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
 
-    // SNAPSHOT is required because of plain-java support
-    // See https://github.com/michel-kraemer/citeproc-java/issues/92 for details
-    implementation 'de.undercouch:citeproc-java:3.0.0-SNAPSHOT'
+    implementation 'de.undercouch:citeproc-java:3.0.0-alpha.1'
 
     implementation group: 'jakarta.activation', name: 'jakarta.activation-api', version: '1.2.1'
     implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '2.3.2'
@@ -228,10 +226,10 @@ dependencies {
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.7.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.7.2'
 
-    testImplementation 'net.bytebuddy:byte-buddy-parent:1.11.1'
+    testImplementation 'net.bytebuddy:byte-buddy-parent:1.11.2'
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
-    testImplementation 'org.mockito:mockito-core:3.11.0'
+    testImplementation 'org.mockito:mockito-core:3.11.1'
     testImplementation 'org.xmlunit:xmlunit-core:2.8.2'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.8.2'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.19.0'

buildres/csl/csl-styles/acta-anaesthesiologica-scandinavica.csl

@@ -155,8 +155,13 @@
   </citation>
   <bibliography second-field-align="flush">
     <layout>
+<<<<<<< HEAD
       <group delimiter=". " suffix=". ">
         <text variable="citation-number"/>
+=======
+      <text variable="citation-number" suffix=". "/>
+      <group delimiter=". " suffix=". ">
+>>>>>>> dbb93e7d9be410a475814d5ae49aef83ce158191
         <text macro="author"/>
         <text macro="title"/>
       </group>

buildres/csl/csl-styles/acta-universitatis-agriculturae-sueciae.csl

@@ -4,19 +4,18 @@
     <title>Acta Universitatis Agriculturae Sueciae (Swedish University of Agricultural Sciences)</title>
     <id>http://www.zotero.org/styles/acta-universitatis-agriculturae-sueciae</id>
     <link href="http://www.zotero.org/styles/acta-universitatis-agriculturae-sueciae" rel="self"/>
-    <link href="https://www.slu.se/en/subweb/library/write-and-cite2/writing-references/referencelist-according-to-the-harvard-system/" rel="documentation"/>
-    <link href="https://www.slu.se/site/bibliotek/skriva-och-referera/skriva-referenser/referenslista-enligt-harvard/" rel="documentation"/>
+    <link href="https://www.slu.se/en/subweb/library/write-and-cite/writing-references/referenslista-enligt-harvard/" rel="documentation"/>
+    <link href="https://www.slu.se/en/subweb/library/write-and-cite/writing-references/in-text-citations-using-the-harvard-system/" rel="documentation"/>
     <author>
       <name>Rintze Zelle</name>
       <uri>http://twitter.com/rintzezelle</uri>
     </author>
     <contributor>
       <name>Patrick O'Brien</name>
-      <uri>https://twitter.com/patobrien333/</uri>
     </contributor>
     <category citation-format="author-date"/>
     <summary>Style as per the May 2019 guidelines.</summary>
-    <updated>2019-05-23T13:14:19+00:00</updated>
+    <updated>2021-04-22T13:05:29+00:00</updated>
     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
   </info>
   <locale xml:lang="en">
@@ -124,15 +123,31 @@
   </macro>
   <macro name="issued">
     <group prefix=" (" suffix=").">
-      <date variable="issued">
-        <date-part name="year"/>
-      </date>
+      <choose>
+        <if match="any" variable="issued">
+          <date variable="issued">
+            <date-part name="year"/>
+          </date>
+        </if>
+        <else>
+          <text term="no date" form="short"/>
+        </else>
+      </choose>
+      <text variable="year-suffix"/>
     </group>
   </macro>
   <macro name="issued-year">
-    <date variable="issued">
-      <date-part name="year"/>
-    </date>
+    <choose>
+      <if variable="issued" match="any">
+        <date variable="issued">
+          <date-part name="year"/>
+        </date>
+      </if>
+      <else>
+        <text term="no date" form="short"/>
+      </else>
+    </choose>
+    <text variable="year-suffix"/>
   </macro>
   <macro name="edition">
     <choose>

buildres/csl/csl-styles/american-chemical-society.csl

@@ -5,7 +5,8 @@
     <title-short>ACS</title-short>
     <id>http://www.zotero.org/styles/american-chemical-society</id>
     <link href="http://www.zotero.org/styles/american-chemical-society" rel="self"/>
-    <link href="https://pubs.acs.org/doi/pdf/10.1021/bk-2006-STYG.ch014" rel="documentation"/>
+    <link href="https://pubs.acs.org/doi/full/10.1021/acsguide.40303" rel="documentation"/>
+    <link href="https://pubs.acs.org/doi/book/10.1021/acsguide" rel="documentation"/>
     <author>
       <name>Julian Onions</name>
       <email>julian.onions@gmail.com</email>
@@ -20,7 +21,7 @@
     <category citation-format="numeric"/>
     <category field="chemistry"/>
     <summary>The American Chemical Society style</summary>
-    <updated>2020-03-10T12:00:00+00:00</updated>
+    <updated>2021-05-22T12:00:00+00:00</updated>
     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
   </info>
   <locale xml:lang="en">
@@ -253,9 +254,9 @@
             <text variable="title"/>
             <text variable="URL"/>
             <date variable="accessed" prefix="(accessed " suffix=")" delimiter=" ">
-              <date-part name="month" form="short" strip-periods="true"/>
-              <date-part name="day" suffix=", "/>
               <date-part name="year"/>
+              <date-part name="month" prefix="-" form="numeric-leading-zeros"/>
+              <date-part name="day" prefix="-" form="numeric-leading-zeros"/>
             </date>
           </group>
         </else-if>

buildres/csl/csl-styles/apa-annotated-bibliography.csl

@@ -14,7 +14,7 @@
     <category citation-format="author-date"/>
     <category field="psychology"/>
     <category field="generic-base"/>
-    <updated>2019-12-04T13:09:49+00:00</updated>
+    <updated>2021-06-10T13:09:49+00:00</updated>
     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
   </info>
   <locale xml:lang="en">
@@ -1860,7 +1860,7 @@
       <text variable="locator"/>
     </group>
   </macro>
-  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true" collapse="year" givenname-disambiguation-rule="primary-name">
+  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true" collapse="year" givenname-disambiguation-rule="primary-name-with-initials">
     <sort>
       <key macro="author-bib" names-min="3" names-use-first="1"/>
       <key macro="date-sort-group"/>

buildres/csl/csl-styles/apa-no-ampersand.csl

@@ -14,7 +14,7 @@
     <category citation-format="author-date"/>
     <category field="psychology"/>
     <category field="generic-base"/>
-    <updated>2019-12-04T13:09:49+00:00</updated>
+    <updated>2021-06-10T13:09:49+00:00</updated>
     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
   </info>
   <locale xml:lang="en">
@@ -1860,7 +1860,7 @@
       <text variable="locator"/>
     </group>
   </macro>
-  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true" collapse="year" givenname-disambiguation-rule="primary-name">
+  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true" collapse="year" givenname-disambiguation-rule="primary-name-with-initials">
     <sort>
       <key macro="author-bib" names-min="3" names-use-first="1"/>
       <key macro="date-sort-group"/>

buildres/csl/csl-styles/apa-single-spaced.csl

@@ -14,7 +14,7 @@
     <category citation-format="author-date"/>
     <category field="psychology"/>
     <category field="generic-base"/>
-    <updated>2019-12-04T13:09:49+00:00</updated>
+    <updated>2021-06-10T13:09:49+00:00</updated>
     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
   </info>
   <locale xml:lang="en">
@@ -1860,7 +1860,7 @@
       <text variable="locator"/>
     </group>
   </macro>
-  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true" collapse="year" givenname-disambiguation-rule="primary-name">
+  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true" collapse="year" givenname-disambiguation-rule="primary-name-with-initials">
     <sort>
       <key macro="author-bib" names-min="3" names-use-first="1"/>
       <key macro="date-sort-group"/>

buildres/csl/csl-styles/apa-with-abstract.csl

@@ -14,7 +14,7 @@
     <category citation-format="author-date"/>
     <category field="psychology"/>
     <category field="generic-base"/>
-    <updated>2019-12-04T13:09:49+00:00</updated>
+    <updated>2021-06-10T13:09:49+00:00</updated>
     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
   </info>
   <locale xml:lang="en">
@@ -1860,7 +1860,7 @@
       <text variable="locator"/>
     </group>
   </macro>
-  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true" collapse="year" givenname-disambiguation-rule="primary-name">
+  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true" collapse="year" givenname-disambiguation-rule="primary-name-with-initials">
     <sort>
       <key macro="author-bib" names-min="3" names-use-first="1"/>
       <key macro="date-sort-group"/>

buildres/csl/csl-styles/apa.csl

@@ -14,7 +14,7 @@
     <category citation-format="author-date"/>
     <category field="psychology"/>
     <category field="generic-base"/>
-    <updated>2019-12-04T13:09:49+00:00</updated>
+    <updated>2021-06-10T13:09:49+00:00</updated>
     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
   </info>
   <locale xml:lang="en">
@@ -1860,7 +1860,7 @@
       <text variable="locator"/>
     </group>
   </macro>
-  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true" collapse="year" givenname-disambiguation-rule="primary-name">
+  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true" collapse="year" givenname-disambiguation-rule="primary-name-with-initials">
     <sort>
       <key macro="author-bib" names-min="3" names-use-first="1"/>
       <key macro="date-sort-group"/>